The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

Shuichiro Imai, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Hiroshi Hori, Nobuyoshi Shimizu

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Evolution of the genome size in eukaryotes is often affected by changes in the noncoding sequences, for which insertions and deletions (indels) of small nucleotide sequences and amplification of repetitive elements are considered responsible. In this study, we compared the genomic DNA sequences of two kinds of fish, medaka (Oryzias latipes) and fugu (Takifugu rubripes), which show two-fold difference in the genome size (800 Mb vs. 400 Mb). We selected a contiguous DNA sequence of 790 kb from the medaka chromosome LG22 (linkage group 22), and made a precise comparison with the sequence (387 kb) of the corresponding region of Takifugu. The sequence of 178 kb in total was aligned common between two fishes, and the remaining sequences (612 kb for medaka and 209 kb for fugu) were found abundant in various repetitive elements including many types of unclassified low copy repeats, all of which accounted for more than a half (54%) of the genome size difference. Furthermore, we identified a significant difference in the length ratio of the unaligned sequences that locate between the aligned sequences (USBAS), particularly after eliminating known repetitive elements. These USBAS with no repetitive elements (USBAS-nr) located within the intron and intergenic region. These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size.

Original languageEnglish
Pages (from-to)135-144
Number of pages10
JournalGenes and Genetic Systems
Volume82
Issue number2
DOIs
Publication statusPublished - 2007

Fingerprint

Takifugu
Oryzias
Takifugu rubripes
Genome Size
Oryzias latipes
Genes
genome
DNA sequences
nucleotide sequences
Fish
Amplification
Fishes
Genomic Segmental Duplications
Intergenic DNA
Sequence Deletion
Nucleic Acid Repetitive Sequences
Insertional Mutagenesis
Chromosomes
Eukaryota
intergenic DNA

Keywords

  • Genome size evolution
  • Indels
  • Medaka
  • Repetitive element
  • Takifugu

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Genetics(clinical)

Cite this

The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes). / Imai, Shuichiro; Sasaki, Takashi; Shimizu, Atsushi; Asakawa, Shuichi; Hori, Hiroshi; Shimizu, Nobuyoshi.

In: Genes and Genetic Systems, Vol. 82, No. 2, 2007, p. 135-144.

Research output: Contribution to journalArticle

Imai, Shuichiro ; Sasaki, Takashi ; Shimizu, Atsushi ; Asakawa, Shuichi ; Hori, Hiroshi ; Shimizu, Nobuyoshi. / The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes). In: Genes and Genetic Systems. 2007 ; Vol. 82, No. 2. pp. 135-144.
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